From effebd90050efaec0155f959ca431c73982c9957 Mon Sep 17 00:00:00 2001
From: sebherbert <sherbert@pasteur.fr>
Date: Thu, 31 Oct 2019 19:02:52 +0100
Subject: [PATCH] Adapt for previous changes
---
MainScripts/surface3D_combine.m | 28 +++++++++++++++-------------
1 file changed, 15 insertions(+), 13 deletions(-)
diff --git a/MainScripts/surface3D_combine.m b/MainScripts/surface3D_combine.m
index 5db22a7..f67a3c4 100644
--- a/MainScripts/surface3D_combine.m
+++ b/MainScripts/surface3D_combine.m
@@ -46,7 +46,7 @@ if nargin == 0
% Define axial step size (in um)
PARAMS.imSettings.axPixSize = 0.5; % axial voxel size (in um)
- PARAMS.imSettings.latPixSize = 0.2076; % lateral voxel size (in um)
+ PARAMS.imSettings.latPixSize = 0.183; % lateral voxel size (in um)
PARAMS.maxTiffImSize = 40000; % Limit the input image size when using an elevation map (in pix)
PARAMS.maxFaces = 300; % If need be, reduce the maximum number of faces for the mesh
@@ -190,7 +190,7 @@ dataCells = checkCoverage(dataCells, dataCurv, dataSeg, PARAMS);
dataCells = cell2ellipse(dataCells, dataCurv, PARAMS);
%% Create a table output
-[tableOutputDeproj, tableOutputBell] = formatTableOuputSurfaceCombine(dataCells, dataSeg);
+tableOutputDeproj = formatTableOuputSurfaceCombine(dataCells, dataSeg);
%% Saving output
save([PARAMS.outputFolder filesep 'deprojectedData.mat'],...
@@ -629,19 +629,21 @@ for bioCell = 1:numel(dataCells.cellIdx)
end
dataCells.cellContour3D = dataCells.cellContour3D';
-% And the 2D sides on the mesh
-dataCells.VERTICES.XYZs = zeros(size(dataSeg.VERTICES.XYs,1),3);
-dataCells.VERTICES.XYZs = dataSeg.VERTICES.XYs;
-for vertex = 1:length(dataCells.VERTICES.vertexOnFace)
- if dataCells.VERTICES.vertexOnFace(vertex)==0
- % when the vertex is not under the mesh, keep its z position at 0
- continue
+if PARAMS.deployJunctNet
+ % And the 2D sides on the mesh
+ dataCells.VERTICES.XYZs = zeros(size(dataSeg.VERTICES.XYs,1),3);
+ dataCells.VERTICES.XYZs = dataSeg.VERTICES.XYs;
+ for vertex = 1:length(dataCells.VERTICES.vertexOnFace)
+ if dataCells.VERTICES.vertexOnFace(vertex)==0
+ % when the vertex is not under the mesh, keep its z position at 0
+ continue
+ end
+ dataCells.VERTICES.XYZs(vertex,3) = horzcat(dataCells.VERTICES.XYZs(vertex,1:2),ones(1)) * ...
+ dataCurv.planeCoefPerFace(dataCells.VERTICES.vertexOnFace(vertex),:)';
end
- dataCells.VERTICES.XYZs(vertex,3) = horzcat(dataCells.VERTICES.XYZs(vertex,1:2),ones(1)) * ...
- dataCurv.planeCoefPerFace(dataCells.VERTICES.vertexOnFace(vertex),:)';
-end
-displayDeprojected(PARAMS,dataCurv,dataCells)
+ displayDeprojected(PARAMS,dataCurv,dataCells)
+end
end
--
GitLab